CancerMutationAnalysis

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see CancerMutationAnalysis.

Cancer mutation analysis

Bioconductor version: 3.0

This package implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver genes (which play an active role in tumorigenesis) and passenger genes (which are mutated in tumor samples, but have no role in tumorigenesis) and incorporate a two-stage study design. The gene-set methods implement a patient-oriented approach, which calculates gene-set scores for each sample, then combines them across samples; a gene-oriented approach which uses the Wilcoxon test is also provided for comparison.

Author: Giovanni Parmigiani, Simina M. Boca

Maintainer: Simina M. Boca <simina.boca at nih.gov>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CancerMutationAnalysis")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CancerMutationAnalysis")

Details

Package Archives

Follow Installation instructions to use this package in your R session.